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<!-- 2022-03-11 Fri 12:54 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-03-11 Fri 12:54 -->
<!-- 2022-04-13 Wed 14:40 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org29e1b1d">1. Accessing sparse quantities</a>
<li><a href="#orgb52be26">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orgacd44e2">1.1. Fortran</a>
<li><a href="#org64925a5">1.1. Fortran</a>
<ul>
<li><a href="#org1ed3f46">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb06a343">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd6fcb73">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd070d3e">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org441fe30">1.1.5. Allocate memory</a></li>
<li><a href="#org0f5e34c">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org5cf89ee">1.1.7. Read two-electron quantities</a>
<li><a href="#orgafc7f4c">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orge3620d4">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf770b43">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orga9abfd7">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgf8f96eb">1.1.5. Allocate memory</a></li>
<li><a href="#org532fc04">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org2620568">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgdf7df26">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1e875c6">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orge3536c8">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgdf25aec">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org5810d9f">1.1.8. Compute the energy</a></li>
<li><a href="#orgbb6b48d">1.1.9. Terminate</a></li>
<li><a href="#org8977f5e">1.1.8. Compute the energy</a></li>
<li><a href="#org028f8ba">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org29e1b1d" class="outline-2">
<h2 id="org29e1b1d"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgb52be26" class="outline-2">
<h2 id="orgb52be26"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgacd44e2" class="outline-3">
<h3 id="orgacd44e2"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org64925a5" class="outline-3">
<h3 id="org64925a5"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org1ed3f46" class="outline-4">
<h4 id="org1ed3f46"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgafc7f4c" class="outline-4">
<h4 id="orgafc7f4c"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgb06a343" class="outline-4">
<h4 id="orgb06a343"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orge3620d4" class="outline-4">
<h4 id="orge3620d4"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgd6fcb73" class="outline-4">
<h4 id="orgd6fcb73"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf770b43" class="outline-4">
<h4 id="orgf770b43"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgd070d3e" class="outline-4">
<h4 id="orgd070d3e"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orga9abfd7" class="outline-4">
<h4 id="orga9abfd7"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org441fe30" class="outline-4">
<h4 id="org441fe30"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-orgf8f96eb" class="outline-4">
<h4 id="orgf8f96eb"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org0f5e34c" class="outline-4">
<h4 id="org0f5e34c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org532fc04" class="outline-4">
<h4 id="org532fc04"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org5cf89ee" class="outline-4">
<h4 id="org5cf89ee"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org2620568" class="outline-4">
<h4 id="org2620568"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgdf7df26" class="outline-5">
<h5 id="orgdf7df26"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orge3536c8" class="outline-5">
<h5 id="orge3536c8"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org1e875c6" class="outline-5">
<h5 id="org1e875c6"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgdf25aec" class="outline-5">
<h5 id="orgdf25aec"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org5810d9f" class="outline-4">
<h4 id="org5810d9f"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org8977f5e" class="outline-4">
<h4 id="org8977f5e"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgbb6b48d" class="outline-4">
<h4 id="orgbb6b48d"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org028f8ba" class="outline-4">
<h4 id="org028f8ba"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-03-11 Fri 12:54 -->
<!-- 2022-04-13 Wed 14:40 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<head>
<!-- 2022-03-11 Fri 12:54 -->
<!-- 2022-04-13 Wed 14:40 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,22 +311,22 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org365eb16">1. Template for HDF5 definitions</a></li>
<li><a href="#org2767730">2. Template for HDF5 structures</a></li>
<li><a href="#org9e16a26">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org0162385">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgcb1e5bd">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8bd2b5e">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orga83dd5a">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org03c0bc2">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc28c99a">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8b88da2">10. Helper functions</a></li>
<li><a href="#org7a167a8">1. Template for HDF5 definitions</a></li>
<li><a href="#org75e825e">2. Template for HDF5 structures</a></li>
<li><a href="#org379bf6e">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org3c56df5">4. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org98b03bd">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org5727110">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgca656f6">7. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgba53933">8. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb0b0234">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org433ad94">10. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org365eb16" class="outline-2">
<h2 id="org365eb16"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org7a167a8" class="outline-2">
<h2 id="org7a167a8"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -338,8 +338,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org2767730" class="outline-2">
<h2 id="org2767730"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org75e825e" class="outline-2">
<h2 id="org75e825e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
@ -352,8 +352,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org9e16a26" class="outline-2">
<h2 id="org9e16a26"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org379bf6e" class="outline-2">
<h2 id="org379bf6e"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -456,8 +456,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org0162385" class="outline-2">
<h2 id="org0162385"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org3c56df5" class="outline-2">
<h2 id="org3c56df5"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -560,8 +560,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgcb1e5bd" class="outline-2">
<h2 id="orgcb1e5bd"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org98b03bd" class="outline-2">
<h2 id="org98b03bd"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -694,8 +694,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org8bd2b5e" class="outline-2">
<h2 id="org8bd2b5e"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org5727110" class="outline-2">
<h2 id="org5727110"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -717,7 +717,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">index_dtype</span>;
<span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span> = <span style="color: #008b8b;">NULL</span>;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span>;
<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">size_ranked</span> = (<span style="color: #228b22;">uint64_t</span>) size * $group_dset_rank$;
/* <span style="color: #b22222;">Determine the optimal type for storing indices depending on the size_max (usually mo_num or ao_num) </span>*/
<span style="color: #a020f0;">if</span> (size_max &lt; UINT8_MAX) {
@ -737,7 +737,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
index_p = index;
index_dtype = H5T_NATIVE_UINT16;
} <span style="color: #a020f0;">else</span> {
index_p = (<span style="color: #228b22;">int32_t</span>*) index_sparse;
index_p = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span>*) index_sparse;
index_dtype = H5T_NATIVE_INT32;
}
@ -896,8 +896,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orga83dd5a" class="outline-2">
<h2 id="orga83dd5a"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgca656f6" class="outline-2">
<h2 id="orgca656f6"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1094,8 +1094,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org03c0bc2" class="outline-2">
<h2 id="org03c0bc2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgba53933" class="outline-2">
<h2 id="orgba53933"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1221,8 +1221,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orgc28c99a" class="outline-2">
<h2 id="orgc28c99a"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb0b0234" class="outline-2">
<h2 id="orgb0b0234"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-9">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1262,8 +1262,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org8b88da2" class="outline-2">
<h2 id="org8b88da2"><span class="section-number-2">10</span> Helper functions</h2>
<div id="outline-container-org433ad94" class="outline-2">
<h2 id="org433ad94"><span class="section-number-2">10</span> Helper functions</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1524,7 +1524,7 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-03-11 Fri 12:54 -->
<!-- 2022-04-13 Wed 14:40 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge60f291">1. TEXT back end</a>
<li><a href="#org5b833fc">1. TEXT back end</a>
<ul>
<li><a href="#org262b8be">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org538aa5a">1.2. Template for general structure in text back end</a></li>
<li><a href="#org183d11d">1.3. Initialize function (constant part)</a></li>
<li><a href="#org645e4c0">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgdba238b">1.5. Template for text read a group</a></li>
<li><a href="#org20ee9d7">1.6. Template for text flush a group</a></li>
<li><a href="#org7c3aa5e">1.7. Template for text free memory</a></li>
<li><a href="#orgca242c4">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgbfc74fc">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org7e79bd9">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orga3f41cb">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org83e4363">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orga67ea82">1.13. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orga30ee45">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org91e9c45">1.2. Template for general structure in text back end</a></li>
<li><a href="#org633d4d5">1.3. Initialize function (constant part)</a></li>
<li><a href="#org12fe8bb">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orga3c5bca">1.5. Template for text read a group</a></li>
<li><a href="#org01f0f8a">1.6. Template for text flush a group</a></li>
<li><a href="#orgf5681e4">1.7. Template for text free memory</a></li>
<li><a href="#orga35665f">1.8. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org07daeef">1.9. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgf307d5b">1.10. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org61baf9b">1.11. Template for has/read/write a string attribute</a></li>
<li><a href="#org1699abb">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org71c7d7f">1.13. Template for text delete a group (UNSAFE mode)</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orge60f291" class="outline-2">
<h2 id="orge60f291"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org5b833fc" class="outline-2">
<h2 id="org5b833fc"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1">
<p>
The "file" produced by the text back end is a directory with one
@ -354,8 +354,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org262b8be" class="outline-3">
<h3 id="org262b8be"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orga30ee45" class="outline-3">
<h3 id="orga30ee45"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -374,8 +374,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org538aa5a" class="outline-3">
<h3 id="org538aa5a"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org91e9c45" class="outline-3">
<h3 id="org91e9c45"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_text_s</span> {
@ -388,8 +388,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org183d11d" class="outline-3">
<h3 id="org183d11d"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org633d4d5" class="outline-3">
<h3 id="org633d4d5"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -532,8 +532,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org645e4c0" class="outline-3">
<h3 id="org645e4c0"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org12fe8bb" class="outline-3">
<h3 id="org12fe8bb"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -555,8 +555,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgdba238b" class="outline-3">
<h3 id="orgdba238b"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div id="outline-container-orga3c5bca" class="outline-3">
<h3 id="orga3c5bca"><span class="section-number-3">1.5</span> Template for text read a group</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -857,8 +857,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org20ee9d7" class="outline-3">
<h3 id="org20ee9d7"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div id="outline-container-org01f0f8a" class="outline-3">
<h3 id="org01f0f8a"><span class="section-number-3">1.6</span> Template for text flush a group</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -922,8 +922,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org7c3aa5e" class="outline-3">
<h3 id="org7c3aa5e"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgf5681e4" class="outline-3">
<h3 id="orgf5681e4"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -970,8 +970,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgca242c4" class="outline-3">
<h3 id="orgca242c4"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div id="outline-container-orga35665f" class="outline-3">
<h3 id="orga35665f"><span class="section-number-3">1.8</span> Template for has/read/write a numerical attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1034,8 +1034,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgbfc74fc" class="outline-3">
<h3 id="orgbfc74fc"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div id="outline-container-org07daeef" class="outline-3">
<h3 id="org07daeef"><span class="section-number-3">1.9</span> Template for has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1131,8 +1131,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org7e79bd9" class="outline-3">
<h3 id="org7e79bd9"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div id="outline-container-orgf307d5b" class="outline-3">
<h3 id="orgf307d5b"><span class="section-number-3">1.10</span> Template for has/read/write a dataset of strings</h3>
<div class="outline-text-3" id="text-1-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1233,8 +1233,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga3f41cb" class="outline-3">
<h3 id="orga3f41cb"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div id="outline-container-org61baf9b" class="outline-3">
<h3 id="org61baf9b"><span class="section-number-3">1.11</span> Template for has/read/write a string attribute</h3>
<div class="outline-text-3" id="text-1-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1308,8 +1308,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org83e4363" class="outline-3">
<h3 id="org83e4363"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org1699abb" class="outline-3">
<h3 id="org1699abb"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1583,8 +1583,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orga67ea82" class="outline-3">
<h3 id="orga67ea82"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div id="outline-container-org71c7d7f" class="outline-3">
<h3 id="org71c7d7f"><span class="section-number-3">1.13</span> Template for text delete a group (UNSAFE mode)</h3>
<div class="outline-text-3" id="text-1-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1615,7 +1615,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

View File

@ -8,7 +8,7 @@
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" />
#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate
#+STARTUP: align nodlcheck hidestars oddeven lognotestate
#+AUTHOR: TREX-CoE
#+LANGUAGE: en

210
trex.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-03-11 Fri 12:54 -->
<!-- 2022-04-13 Wed 14:40 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,33 +333,34 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org56d8986">1. Metadata (metadata group)</a></li>
<li><a href="#orgb1f499e">2. Electron (electron group)</a></li>
<li><a href="#org5cc8a82">3. Nucleus (nucleus group)</a></li>
<li><a href="#org35661b1">4. Effective core potentials (ecp group)</a>
<li><a href="#org43da47e">1. Metadata (metadata group)</a></li>
<li><a href="#org6992d6e">2. Electron (electron group)</a></li>
<li><a href="#orgabfd33b">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgce25685">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgf0c1d1a">4.1. Example</a></li>
<li><a href="#org048c36b">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgddc4bdf">5. Basis set (basis group)</a>
<li><a href="#orgd8244eb">5. Basis set (basis group)</a>
<ul>
<li><a href="#orge85c802">5.1. Example</a></li>
<li><a href="#org5412e10">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org25757ac">6. Atomic orbitals (ao group)</a>
<li><a href="#org1baedc9">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgb2e4d24">7. Molecular orbitals (mo group)</a>
<li><a href="#org8adb423">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org2a64258">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgc2bf608">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgb5fa684">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd0a95a6">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org02d15d9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9a6fddf">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org8c5ddc1">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orga4cddb0">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org5b8bdc9">10. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -367,18 +368,12 @@ for the JavaScript code in this tag.
This page contains information about the general structure of the
TREXIO library. The source code of the library can be automatically
generated based on the contents of the <code>trex.json</code> configuration file,
which itself is compiled from different sections (groups) presented
which itself is generated from different sections (groups) presented
below.
</p>
<p>
For more information about the automatic generation on the source code
or regarding possible modifications, please contact the TREXIO
developers.
</p>
<p>
All quantities are saved in TREXIO file in atomic units. The
All quantities are saved in TREXIO files in atomic units. The
dimensions of the arrays in the tables below are given in column-major
order (as in Fortran), and the ordering of the dimensions is reversed
in the produced <code>trex.json</code> configuration file as the library is
@ -389,7 +384,7 @@ written in C.
TREXIO currently supports <code>int</code>, <code>float</code> and <code>str</code> types for both
single attributes and arrays. Note, that some attributes might have
<code>dim</code> type (e.g. <code>num</code> of the <code>nucleus</code> group). This type is treated
exactly the same as <code>int</code> with the only difference that <code>dim</code>
exactly in the same way as <code>int</code> with the only difference that <code>dim</code>
variables cannot be negative. This additional constraint is required
because <code>dim</code> attributes are used internally to allocate memory and to
check array boundaries in the memory-safe API. Most of the times, the
@ -397,8 +392,8 @@ check array boundaries in the memory-safe API. Most of the times, the
</p>
<p>
In Fortran, the arrays are 1-based and in most other languages the
arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
In Fortran, arrays are 1-based and in most other languages the
arrays are 0-based. Hence, we introduce the <code>index</code> type which is a
1-based <code>int</code> in the Fortran interface and 0-based otherwise.
</p>
@ -406,11 +401,13 @@ arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
For sparse data structures such as electron replusion integrals,
the data can be too large to fit in memory and the data needs to be
fetched using multiple function calls to perform I/O on buffers.
For more information on how to read/write sparse data structures, see
the <a href="./examples.html">examples</a>.
</p>
<div id="outline-container-org56d8986" class="outline-2">
<h2 id="org56d8986"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org43da47e" class="outline-2">
<h2 id="org43da47e"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -420,7 +417,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org73b5985" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbbe7e1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -501,15 +498,15 @@ then the <code>unsafe</code> attribute value can be manually overwritten (in uns
</div>
</div>
<div id="outline-container-orgb1f499e" class="outline-2">
<h2 id="orgb1f499e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org6992d6e" class="outline-2">
<h2 id="org6992d6e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="orgff31774" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbe41d44" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -530,6 +527,13 @@ the number of &uarr; and &darr; electrons is fixed.
</tr>
</thead>
<tbody>
<tr>
<td class="org-left"><code>num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of electrons</td>
</tr>
<tr>
<td class="org-left"><code>up_num</code></td>
<td class="org-left"><code>int</code></td>
@ -548,15 +552,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org5cc8a82" class="outline-2">
<h2 id="org5cc8a82"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orgabfd33b" class="outline-2">
<h2 id="orgabfd33b"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgc04c3a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc4f4b69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -623,8 +627,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org35661b1" class="outline-2">
<h2 id="org35661b1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgce25685" class="outline-2">
<h2 id="orgce25685"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -657,7 +661,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orge084345" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc6c6f68" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -759,8 +763,8 @@ If you encounter the aforementioned issue, please report it to our <a href="http
</p>
</div>
<div id="outline-container-orgf0c1d1a" class="outline-3">
<h3 id="orgf0c1d1a"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org048c36b" class="outline-3">
<h3 id="org048c36b"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -823,8 +827,8 @@ power = [
</div>
</div>
<div id="outline-container-orgddc4bdf" class="outline-2">
<h2 id="orgddc4bdf"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orgd8244eb" class="outline-2">
<h2 id="orgd8244eb"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -877,7 +881,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="orga494916" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org270f4b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -971,8 +975,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orge85c802" class="outline-3">
<h3 id="orge85c802"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org5412e10" class="outline-3">
<h3 id="org5412e10"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1050,8 +1054,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org25757ac" class="outline-2">
<h2 id="org25757ac"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org1baedc9" class="outline-2">
<h2 id="org1baedc9"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1104,13 +1108,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgddc4bdf">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgd8244eb">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p>
<table id="org2b3af66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd4885d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1162,8 +1166,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org1268404" class="outline-3">
<h3 id="ao_one_e"><a id="org1268404"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgdb31d9f" class="outline-3">
<h3 id="ao_one_e"><a id="orgdb31d9f"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1180,7 +1184,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org1589284" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd7a5387" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1240,8 +1244,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgdb9d958" class="outline-3">
<h3 id="ao_two_e"><a id="orgdb9d958"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org8ab253a" class="outline-3">
<h3 id="ao_two_e"><a id="org8ab253a"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1262,7 +1266,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orgd34360c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org24e2de2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1302,10 +1306,10 @@ notation.
</div>
</div>
<div id="outline-container-orgb2e4d24" class="outline-2">
<h2 id="orgb2e4d24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org8adb423" class="outline-2">
<h2 id="org8adb423"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgfc34de6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6a35a08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1371,8 +1375,8 @@ notation.
</table>
</div>
<div id="outline-container-org2a64258" class="outline-3">
<h3 id="org2a64258"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgb5fa684" class="outline-3">
<h3 id="orgb5fa684"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1380,7 +1384,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3d74cc1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org22b4a6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1440,8 +1444,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgc2bf608" class="outline-3">
<h3 id="orgc2bf608"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgd0a95a6" class="outline-3">
<h3 id="orgd0a95a6"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1449,7 +1453,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3bab743" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org848a240" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1489,11 +1493,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org02d15d9" class="outline-2">
<h2 id="org02d15d9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org8c5ddc1" class="outline-2">
<h2 id="org8c5ddc1"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org9a6fddf" class="outline-2">
<h2 id="org9a6fddf"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orga4cddb0" class="outline-2">
<h2 id="orga4cddb0"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1546,7 +1550,7 @@ The total energy can be computed as:
\]
</p>
<table id="org46f5bb4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2755768" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1626,10 +1630,78 @@ The total energy can be computed as:
</table>
</div>
</div>
<div id="outline-container-org5b8bdc9" class="outline-2">
<h2 id="org5b8bdc9"><span class="section-number-2">10</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-10">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
at points of the 3N-dimensional space. Some algorithms require multiple
independent <i>walkers</i>, so it is possible to store multiple coordinates,
as well as some quantities evaluated at those points.
</p>
<p>
By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orgf08a6c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<thead>
<tr>
<th scope="col" class="org-left">Variable</th>
<th scope="col" class="org-left">Type</th>
<th scope="col" class="org-left">Dimensions</th>
<th scope="col" class="org-left">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td class="org-left"><code>num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of 3N-dimensional points</td>
</tr>
<tr>
<td class="org-left"><code>point</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(3, electron.num, qmc.num)</code></td>
<td class="org-left">3N-dimensional points</td>
</tr>
<tr>
<td class="org-left"><code>psi</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(qmc.num)</code></td>
<td class="org-left">Wave function evaluated at the points</td>
</tr>
<tr>
<td class="org-left"><code>e_loc</code></td>
<td class="org-left"><code>float</code></td>
<td class="org-left"><code>(qmc.num)</code></td>
<td class="org-left">Local energy evaluated at the points</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-03-11 Fri 12:54</p>
<p class="date">Created: 2022-04-13 Wed 14:40</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>